Pathogenic bacteria secrete various virulence factors as their biochemical weapons to gain access to and destroy the target cells. They can directly interact with the outer lipid bilayer membrane of eukaryotic cells, inducing the premature cell death by either apoptosis or necrosis. Such virulence factors account for much of the toxic actions associated with bacterial infection; therefore the detection of such proteins could provide a methodology for sensing/detection of pathogenic bacteria in, for example, food or human tissue. Detection and identification of pathogenic bacteria by conventional methods such as plating and counting in laboratory is expensive and time consuming. With growing concerns over emergence and re-emergence of pathogenic bacteria with high resistant to current antibiotics, there is a potential need for effective detection of pathogenic toxins invitro. On the other hand, artificially prepared lipid bilayer membrane on planar metallic surfaces provides the cell membrane mimics which are extremely useful in exploring the cellular functions and processes at the molecular level. Therefore in this work, an application of planar tethered bilayer lipid membrane (pTBLM) as a biomimetic sensing platform for the detection of clinically important pathogens, Staphylococcus aureus and Pseudomonas aeruginosa via their secreted virulence factors was presented. Planar TBLM was modified by incorporation of cholesterol and detection of bacterial toxins at human body temperature was examined by impedance and surface plasmon resonance methods. The results of pathogenic bacterial toxin detection were compared with those of Escherichia coli (DH5α), the human gut normal flora with non-pathogenic strain, as a control. Additionally pTBLM was transferred onto single nanoporous Si3N4 membrane to enhance the toxin sensitivity and extend the lifetime for the possible realization of future membrane chips for ion channel characterizations and drug screenings. Then the single ion channel measurement was demonstrated with nanopore-suspended TBLM (Nano-psTBLM) using α-toxin of S. aureus. The results presented in this work therefore, may pave the more effective and efficient ways for future pathogenic bacterial detection in which the sensing mechanism was solely based on the nature of interactions as well as modes of action between bacterial toxins and artificial lipid bilayer membranes.

The goals of this work were to synthesize high performance perovskite based thin film solid oxide fuel cell (TF-SOFC) cathodes by pulsed laser deposition (PLD), to study the structural, electrical and electrochemical properties of these cathodes and to establish structure-property relations for these cathodes in order to further improve their properties and design new structures. Nanostructured cathode thin films with vertically-aligned nanopores (VANP) were processed using PLD. These VANP structures enhance the oxygen-gas phase diffusivity, thus improve the overall TF-SOFC performance. La0.5Sr0.5CoO3 (LSCO) and La0.4Sr0.6Co0.8Fe0.2O3 (LSCFO) were deposited on various substrates (YSZ, Si and pressed Ce0.9Gd0.1O1.95 (CGO) disks). Microstructures and properties of the nanostructured cathodes were characterized by transmission electron microscope (TEM), high resolution TEM (HRTEM), scanning electron microscope (SEM) and electrochemical impedance spectroscopy (EIS) measurements. A thin layer of vertically-aligned nanocomposite (VAN) structure was deposited in between the CGO electrolyte and the thin film LSCO cathode layer for TF-SOFCs. The VAN structure consists of the electrolyte and the cathode materials in the composition of (CGO) 0.5 (LSCO) 0.5. The self-assembled VAN nanostructures contain highly ordered alternating vertical columns formed through a one-step thin film deposition using a PLD technique. These VAN structures significantly increase the interface area between the electrolyte and the cathode as well as the area of active triple phase boundary (TPB), thus improving the overall TF-SOFC performance at low temperatures, as low as 400oC, demonstrated by EIS measurements. In addition, the binary VAN interlayer could act as the transition layer that improves the adhesion and relieves the thermal stress and lattice strain between the cathode and the electrolyte. The microstructural properties and growth mechanisms of CGO thin film prepared by PLD technique were investigated. Thin film CGO electrolytes with different grain sizes and crystal structures were prepared on single crystal YSZ substrates under different deposition conditions. The effect of the deposition conditions such as substrate temperature and laser ablation energy on the microstructural properties of these films are examined using XRD, TEM, SEM, and optical microscope. CGO thin film deposited above 500 ºC starts to show epitaxial growth on YSZ substrates. The present study suggests that substrate temperature significantly influences the microstructure of the films especially film grain size.

abstract: Driven by the curiosity for the secret of life, the effort on sequencing of DNAs and other large biopolymers has never been respited. Advanced from recent sequencing techniques, nanotube and nanopore based sequencing has been attracting much attention. This thesis focuses on the study of first and crucial compartment of the third generation sequencing technique, the capture and translocation of biopolymers, and discuss the advantages and obstacles of two different nanofluidic pathways, nanotubes and nanopores for single molecule capturing and translocation. Carbon nanotubes with its constrained structure, the frictionless inner wall and strong electroosmotic flow, are promising materials for linearly threading DNA and other biopolymers for sequencing. Solid state nanopore on the other hand, is a robust chemical, thermal and mechanical stable nanofluidic device, which has a high capturing rate and, to some extent, good controllable threading ability for DNA and other biomolecules. These two different but similar nanofluidic pathways both provide a good preparation of analyte molecules for the sequencing purpose. In addition, more and more research interests have move onto peptide chains and protein sensing. For proteome is better and more direct indicators for human health, peptide chains and protein sensing have a much wider range of applications on bio-medicine, disease early diagnoses, and etc. A universal peptide chain nanopore sensing technique with universal chemical modification of peptides is discussed in this thesis as well, which unifies the nanopore capturing process for vast varieties of peptides. Obstacles of these nanofluidic pathways are also discussed. In the end of this thesis, a proposal of integration of solid state nanopore and fixed-gap recognition tunneling sequencing technique for a more accurate DNA and peptide readout is discussed, together with some early study work, which gives a new direction for nanopore based sequencing. / Dissertation/Thesis / Doctoral Dissertation Physics 2015

abstract: Engineered nanoporous substrates made using materials such as silicon nitride or silica have been demonstrated to work as particle counters or as hosts for nano-lipid bilayer membrane formation. These mechanically fabricated porous structures have thicknesses of several hundred nanometers up to several micrometers to ensure mechanical stability of the membrane. However, it is desirable to have a three-dimensional structure to ensure increased mechanical stability. In this study, circular silica shells used from Coscinodiscus wailesii, a species of diatoms (unicellular marine algae) were immobilized on a silicon chip with a micrometer-sized aperture using a UV curable polyurethane adhesive. The current conducted by a single nanopore of 40 nm diameter and 50 nm length, during the translocation of a 27 nm polystyrene sphere was simulated using COMSOL multiphysics and tested experimentally. The current conducted by a single 40 nm diameter nanopore of the diatom shell during the translocation of a 27 nm polystyrene sphere was simulated using COMSOL Multiphysics (28.36 pA) and was compared to the experimental measurement (28.69 pA) and Coulter Counting theory (29.95 pA).In addition, a mobility of 1.11 x 10-8 m2s-1V-1 for the 27 nm polystyrene spheres was used to convert the simulated current from spatial dependence to time dependence. To achieve a sensing diameter of 1-2 nanometers, the diatom shells were used as substrates to perform ion-channel reconstitution experiments. The immobilized diatom shell was functionalized using silane chemistry and lipid bilayer membranes were formed. Functionalization of the diatom shell surface improves bilayer formation probability from 1 out of 10 to 10 out of 10 as monitored by impedance spectroscopy. Self-insertion of outer membrane protein OmpF of E.Coli into the lipid membranes could be confirmed using single channel recordings, indicating that nano-BLMs had formed which allow for fully functional porin activity. The results indicate that biogenic silica nanoporous substrates can be simulated using a simplified two dimensional geometry to predict the current when a nanoparticle translocates through a single aperture. With their tiered three-dimensional structure, diatom shells can be used in to form nano-lipid bilayer membranes and can be used in ion-channel reconstitution experiments similar to synthetic nanoporous membranes. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2015

Nanopores have emerged as a simple but effective tool to investigate the behavior of polymers in solution. They have shown great potential to simplify expensive and time consuming procedures like DNA sequencing, protein detection, and disease biomarker detection. With the development of in situ fabrication of solid-state nanopores by controlled breakdown (CBD) of a dielectric material, nanomanufacturing of nanopore-based technologies became feasible. However, there are still a lot of challenges to overcome for these applications to become reality. One of the major problems with solid-state nanopores is the rapid passage time of analytes going through the pore, complicating detection and reliable identification of molecules. In this thesis molecular structures are proposed that increase passage times due to increased interactions between analyte and pore wall, and at the same time increase signal amplitude due to increased blockage of the pore. These structures are short, branched DNA molecules that were assembled with built-in modifications and matching sequences to assume their structure. Nanopore experiments reveal that these structurally defined DNA produce higher detection rates than their linear DNA counterparts, making them better candidates for labels in single-molecule sensing experiments.

No description available.

Anodic aluminum oxide (AAO) nanopores are excellent templates to fabricate different nanostructures. However, the pores are limited to a hexagonal arrangement with a domain size of a few micrometers.  In this dissertation, focused ion beam (FIB) is used to create pre-patterned concaves to guide the anodization. Due to the advantage of FIB lithography, highly ordered AAO arrays with different arrangements, alternating diameters, and periodic pore densities are successfully achieved. Anodization window to fabricate ordered AAO is enlarged due to the FIB pre-pattern guidance. AAO has also been successfully used as a template to nanoimprint prepolymer to synthesize vertically aligned and high aspect ratio h-PDMS nanorod arrays with Moiré pattern arrangements. The formation mechanism of anodic TiO2 nanotubes is proposed in this dissertation. Moreover, FIB pre-pattern guided anodization is introduced to synthesize highly ordered TiO₂ nanotubes with different morphologies. The effects of inter-tube distance and arrangement to the structure of TiO₂ nanotubes are investigated. TiO2 nanotubes with branched and bamboo-type structures are achieved by adjusting anodization voltage. The influence of patterned concave depth and surface curvature on the growth of TiO₂ nanotubes and AAO are studied. The efficiency of TiO₂ nanotubes in supercapacitors and photoelectrochemical water splitting are optimized by enlarging surface area and increasing electrical conductivity. Focused ion beam can not only create concave arrays to guide the electrochemical anodization, but also be used for nanoscale sculpting and 3D analysis. When the TiO₂ nanotube surface is bombarded by FIB, there is a mass transfers due to ion-induced viscous flow and sputter milling, thus the TiO₂ nanotubes are selectively closed and opened. By combining FIB cutting and SEM imaging to create a series of 2D cross section SEM images, 3D reconstruction can be obtained by stacking SEM images together. This 3D reconstruction offers an opportunity to directly and quantitatively observe the pore evolution to understand the sintering process. / Ph. D.

Ce travail de thèse porte sur le contrôle des propriétés de trois systèmes magnéto-plasmoniques grâce à différents types de nanostructuration. Ces structures sont basées respectivement sur la Propagation de Plasmons de Surface (SPP), les Plasmons de Surface Localisés (LSP) et la spectroscopie d’interférences en réflexion (RIfS). La manipulation des propriétés magnéto-optiques (MO) pour une utilisation dans les biocapteurs est discutée. Le premier système est une structure SPP en couche mince de couches de métaux nobles et d’un matériau magnétique de type multicouche présentant une anisotropie uni-axiale contrôlée. L’anisotropie de la couche magnétique se reflète sur les propriétés plasmoniques. Une amélioration de l’activité magnéto-optique peut être mise à profit pour améliorer la sensibilité de capteurs basés sur cette structure. Le second dispositif est une structure LSP avec nanoparticules d’or et d’une couche magnétique continue. Il est démontré qu’une couche diélectrique entre la couche magnétique et les nanoparticules d’or est indispensable pour préserver la résonance plasmonique. L’épaisseur de la couche magnétique a un effet sur cette dernière qui peut en principe être mise à profit pour influer sur l’activité magnéto-optique. La troisième approche est une structure RIfS composée d’un système multicouche magnéto-plasmonique Ag/ITO/CoFeB/ITO/Ag déposé sur un substrat nanoporeux d’oxyde d’aluminium anodique (AAO). Le signal RIfS dépend de la taille et de la longueur des nanopores. Le diamètre des nanopores affecte également la réponse magnéto-optique en réflexion en générant une inversion du signe des cycles d’aimantation mesurés par effet Kerr. / This PhD dissertation deals with the tuning of the magneto-optical (MO) response of three different magnetoplasmonic systems by using different nanostructuration schemes. They are structures based on SPPs, LSPs and RIfS, respectively. The manipulation of MO activity to be used in biosensors and to improve the sensitivity is also discussed. The first system is thin-film SPP structure consisting of magnetic and plasmonic layers, where the magnetic part is nanostructured multilayers with controlled uni-axial anisotropy. The uni-axial anisotropic properties of the multilayered magnetic materials were clearly reflected on the plasmonic properties of the system. An enhancement in the MO activity can be used to improve the sensitivity of the sensors based on this structure. The second system is a LSP-based magnetoplasmonic structure consisting of Au nanoparticle arrays and continuous magnetic layers. It is demonstrated that a dielectric layer in between Au nanoparticles and ferromagnetic layers is indispensable in order to preserve the plasmonic resonance. The thickness of magnetic layers has an effect on the plasmonic property, which can be further used to tune the MO activity. The third system is a hybrid RIfS structure with a magnetoplasmonic multilayer Ag/ITO/CoFeB/ITO/Ag deposited on a nanoporous AAO substrate. The RIfS signal depends on both the size and the length of the nanopores. The diameter of the nanopores also affects the MO response by generating a reversal in the sign of the Kerr loops. This can be viewed as the tuning factor of MO activity of the structure.

O estudo do processo de fusão e solidificação da água contida dentro de materiais confinantes tem sido amplamente discutido em química, biologia, física, geologia, e com diversas aplicações tecnológicas, tais como aplicação na fabricação de etanol de segunda geração, ou etanol celulósico, separação de fases, fabricação de nanomateriais. Pesquisas mostraram que as temperaturas de transição da água nanoconfinada são muito sensíveis ao diâmetro do poro, mas que podem ser pouco afetadas pela natureza, hidrofóbica ou hidrofílica, da superfície do poro. Outra importante constatação em experimentos de fusão e congelamento em nanoporos é que nem toda água presente nos poros pode ser cristalizada até gelo. A existência de uma camada de água pré-fundida em nanoporos tem sido confirmada através de experimentos. Com o objetivo de entender mais profundamente como a temperatura de transição da água confinada depende da natureza da parede confinante e do tamanho do confinamento, propõe-se um modelo de nanoporos de celulose para o confinamento, onde varia-se o diâmetro e comprimento do nanoporo, além da natureza da parede do nanoporo. Nossos estudos, mostram que para sistemas hidrofóbicos, com formação de camada de água líquida na parede, as temperaturas de transição variam desde relativamente baixas, para menores valores de calor latente, até atingindo a temperatura de transição da água bulk, para calor latente mais alto. Enquanto que para sistemas hidrofílicos, para nenhum dos valores de calor latente trabalhados, e para nenhum tamanho do sistema, a temperatura de transição atinge o valor de bulk. / The study of the fusion process and water solidification inside confining materials has been widely discussed in Chemistry, Biology, Physics, and Geology, and has various technological applications as the usage and fabrication of second generation ethanol or cellulosic ethanol, phase separation, and nanomaterials fabrications. Researches have shown that nanoconfined water’s transition temperature are highly sensitive to the pore. Another interesting remark on freezing and fusion experiments on nanopores is that not all water present in pores can be crystallized into ice. The existence of a water layer pre-melted on nanopores has been confirmed through experiments. Aiming at understanding deeply how water’s transition temperature depends on the nature of the confining wall and size, a cellulose nanopore model is proposed to the confinement, where the nanopore diameter and length are varied, besides the nature of the wall of the nanopore. Our studies show that for hydrophobic systems, with the liquid water layer formation on the wall, the transition temperatures vary from relatively low latent heat to smaller values, even reaching the temperature transition on bulk water to higher latent heat. While for hydrophilic systems, for none of the latent heat used and no system size the transition temperature reaches bulk value.

Orientador: Alexandre Reily Rocha / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Nanociências e Materiais Avançados, 2014.